Mercurial > repos > gga > tripal_organism_add_organism
view organism_add_organism.xml @ 7:a2f91a023185 draft default tip
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author | gga |
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date | Wed, 14 Aug 2019 10:02:51 -0400 |
parents | 3ad5a94fb0d8 |
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<?xml version="1.0"?> <tool id="organism_add_organism" profile="16.04" name="Create an organism" version="@WRAPPER_VERSION@.0"> <description>in Tripal</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="1.5">jq</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ @AUTH@ tripaille organism add_organism #if str($description): --comment '$description' #end if #if $infra.use_infra: --infraspecific_rank '$infra.rank' --infraspecific_name '$infra.name' #end if --common '$common' --abbr '$abbr' '$genus' '$species' | jq -S . > '$results' ]]></command> <inputs> <param name="genus" type="text" label="Genus" help="e.g.: Homo" /> <param name="species" argument="--species" type="text" label="Species" help="e.g.: sapiens" /> <param name="abbr" type="text" label="Abbreviation" help="e.g.: H. sapiens" /> <param name="common" type="text" label="Common name" help="e.g.: Human" /> <param name="description" argument="--comment" type="text" label="Description" optional="True"> <expand macro="sanitized"/> </param> <conditional name="infra"> <param name="use_infra" type="boolean" checked="false" label="Specify an infraspecific rank" /> <when value="false"></when> <when value="true"> <param name="rank" argument="--infraspecific_rank" type="select" label="Infraspecific Rank"> <option value="subspecies">subspecies</option> <option value="varietas">varietas</option> <option value="subvariety">subvariety</option> <option value="forma">forma</option> <option value="subforma">subforma</option> </param> <param name="name" argument="--infraspecific_name" type="text" label="Infraspecific Name" help="The infraspecific name of the new organism (e.g. a strain name)" /> </when> </conditional> </inputs> <outputs> <data format="json" name="results" label="New Tripal organism" /> </outputs> <tests> <test expect_failure="true"> <param name="genus" value="Testus" /> <param name="species" value="testum" /> <param name="abbr" value="test" /> <param name="common" value="test stuff" /> <param name="common" value="My cool new test organism" /> <expand macro="test_result" /> </test> <test expect_failure="true"> <param name="genus" value="Testus" /> <param name="species" value="testum" /> <param name="abbr" value="test" /> <param name="common" value="test stuff" /> <param name="common" value="My cool new test organism" /> <conditional name="infra"> <param name="use_infra" value="True" /> <param name="rank" value="subspecies" /> <param name="name" value="strain3" /> </conditional> <expand macro="test_result" /> </test> </tests> <help><![CDATA[ @HELP_OVERVIEW@ **Create Organism** With this tool, you can create a new organism in the Tripal/Chado database @HELP@ ]]></help> <expand macro="citation"/> </tool>